Oh, the message about some of the the schedules being ill-conditioned is 
not an error, it is just letting the user know the proportion of 
randomly selected schedules were bad. In this case, you have quite a 
large number. It should drop when you increase the ntp


On 12/21/2017 10:29 AM, Dirks, Bryce Ronald Alan wrote:
>
> That is the complete terminal and thank you for your help!
>
>
> *Bryce Dirks*
> Research Associate
> Brain Connectivity and Cognition Laboratory
> Department of Psychology
> University of Miami
> Website: http://www.psy.miami.edu/bccl/
> Phone:_ (305)284-3286_
>
>
>
> ------------------------------------------------------------------------
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu 
> <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N Greve 
> <gr...@nmr.mgh.harvard.edu>
> *Sent:* Wednesday, December 20, 2017 6:38:48 PM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] Optseq Help
>  send me the full terminal output that includes the error
>
>
> On 12/20/2017 05:05 PM, Dirks, Bryce Ronald Alan wrote:
> >
> >
> >
> > *Bryce Dirks*
> > Research Associate
> > Brain Connectivity and Cognition Laboratory
> > Department of Psychology
> > University of Miami
> > Website: 
> https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.psy.miami.edu%2Fbccl%2F&data=02%7C01%7Cbrd47%40miami.edu%7Cbc30d90ba26d41b342f508d54802dacc%7C2a144b72f23942d48c0e6f0f17c48e33%7C0%7C0%7C636494099467047925&sdata=iJ9ZPDXEPh7iHgqAUo86dOjilT08bKfJwyVSystzN6c%3D&reserved=0
> > Phone:_ (305)284-3286_
> >
> >
> >
> > ------------------------------------------------------------------------
> > *From:* freesurfer-boun...@nmr.mgh.harvard.edu
> > <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N Greve
> > <gr...@nmr.mgh.harvard.edu>
> > *Sent:* Wednesday, December 20, 2017 4:44:40 PM
> > *To:* freesurfer@nmr.mgh.harvard.edu
> > *Subject:* Re: [Freesurfer] Optseq Help
> > Run
> >
> > optseq2 --all-info
> >
> >
> > and send the result. I think you may be using an older version. I've put
> > the newest version here
> >
> > 
> https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgate.nmr.mgh.harvard.edu%2Fsafelinks%2Fgreve%2Foptseq2&data=02%7C01%7Cbrd47%40miami.edu%7C65c4c935aaba4abb80ce08d547f2eb12%7C2a144b72f23942d48c0e6f0f17c48e33%7C0%7C0%7C636494031019648605&sdata=P%2BtuLgRJMQBV84JfGC6ZyfHtfDFL2QHUKCxiQQ52OBY%3D&reserved=0
> >
> >
> >
> > On 12/20/2017 04:26 PM, Dirks, Bryce Ronald Alan wrote:
> > >
> > > We are not using freesurfer, but just the optseq2 unix script.
> > >
> > >
> > >
> > >
> > >
> > > *Bryce Dirks*
> > > Research Associate
> > > Brain Connectivity and Cognition Laboratory
> > > Department of Psychology
> > > University of Miami
> > > Website:
> > 
> https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.psy.miami.edu%2Fbccl%2F&data=02%7C01%7Cbrd47%40miami.edu%7C65c4c935aaba4abb80ce08d547f2eb12%7C2a144b72f23942d48c0e6f0f17c48e33%7C0%7C0%7C636494031019648605&sdata=35BDgdXblY0KRy07bnFYxqdfwI5NCOkCL%2BcwbiPnBbo%3D&reserved=0
> > > Phone:_ (305)284-3286_
> > >
> > >
> > >
> > > 
> ------------------------------------------------------------------------
> > > *From:* freesurfer-boun...@nmr.mgh.harvard.edu
> > > <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N Greve
> > > <gr...@nmr.mgh.harvard.edu>
> > > *Sent:* Wednesday, December 20, 2017 3:40:48 PM
> > > *To:* freesurfer@nmr.mgh.harvard.edu
> > > *Subject:* Re: [Freesurfer] Optseq Help
> > > Can you send me the terminal output? I ran this command and did not
> > > receive any errors using v6
> > >
> > > optseq2 --ntp 180 --tr 2 --psdwin 0 30 1 --ev flexibility 12 10 --ev
> > > control 12 10 --nsearch 10000 --nkeep 3 --o cFIST_10trials8s_Run1
> > >
> > > what version of FS are you running?
> > >
> > >
> > >
> > > On 12/20/2017 02:29 PM, Dirks, Bryce Ronald Alan wrote:
> > > >
> > > > I also tried reducing the window and that removed the error. I also
> > > > only get the error on a subset of the schedule so if we keep the 
> top 3
> > > >  would they /not/ be ill-conditioned?
> > > >
> > > >
> > > >
> > > > *
> > > > *
> > > > *Bryce Dirks*
> > > > Research Associate
> > > > Brain Connectivity and Cognition Laboratory
> > > > Department of Psychology
> > > > University of Miami
> > > > Website:
> > >
> > 
> https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.psy.miami.edu%2Fbccl%2F&data=02%7C01%7Cbrd47%40miami.edu%7Ce895fb97ad7d43cec71808d547ea050d%7C2a144b72f23942d48c0e6f0f17c48e33%7C0%7C0%7C636493992801342342&sdata=2cVt5PsoucM7H3%2FILIMY8v4sPW0zlZPFjhgd8vYG7g4%3D&reserved=0
> > > > Phone:_ (305)284-3286_
> > > >
> > > >
> > > >
> > > >
> > ------------------------------------------------------------------------
> > > > *From:* Dirks, Bryce Ronald Alan
> > > > *Sent:* Wednesday, December 20, 2017 11:44:03 AM
> > > > *To:* freesurfer@nmr.mgh.harvard.edu
> > > > *Subject:* Re: [Freesurfer] Optseq Help
> > > >
> > > > I added 120 to the ntp make ntp=300, but still got the same error. I
> > > > also tried running a ntp=360 and got the same ill-condtioned
> > statement.
> > > >
> > > >
> > > > *Bryce Dirks*
> > > > Research Associate
> > > > Brain Connectivity and Cognition Laboratory
> > > > Department of Psychology
> > > > University of Miami
> > > > Website:
> > >
> > 
> https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.psy.miami.edu%2Fbccl%2F&data=02%7C01%7Cbrd47%40miami.edu%7Ce895fb97ad7d43cec71808d547ea050d%7C2a144b72f23942d48c0e6f0f17c48e33%7C0%7C0%7C636493992801342342&sdata=2cVt5PsoucM7H3%2FILIMY8v4sPW0zlZPFjhgd8vYG7g4%3D&reserved=0
> > > > Phone:_ (305)284-3286_
> > > >
> > > >
> > > >
> > > >
> > ------------------------------------------------------------------------
> > > > *From:* freesurfer-boun...@nmr.mgh.harvard.edu
> > > > <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N 
> Greve
> > > > <gr...@nmr.mgh.harvard.edu>
> > > > *Sent:* Tuesday, December 19, 2017 6:21:31 PM
> > > > *To:* freesurfer@nmr.mgh.harvard.edu
> > > > *Subject:* Re: [Freesurfer] Optseq Help
> > > > You need to include some time for fixation. Ie, your total run 
> time is
> > > > 180*2=360 sec. The total stimulation time is 12*10*3 = 360 sec.
> > You need
> > > > to increase the length of the fmRI run (or reduce the total 
> number of
> > > > stimuli). Usually I include as much fixation as any other
> > condition. In
> > > > this case, that would be 12*10=120 sec. So try adding 120 sec (ie,
> > > > incrase --ntp 180) and re-run
> > > >
> > > >
> > > > On 12/19/2017 05:21 PM, Dirks, Bryce Ronald Alan wrote:
> > > > >
> > > > > Hello,
> > > > >
> > > > > I am trying to create the optseq for a cognitive flexibility
> > > > > experiment we are conducting. It consists of 10 flexibility, 10
> > > > > control, and 10 fixation trials. The flexibility and control 
> trials
> > > > > are 12 seconds long. Our TR= 2s. We want to ensure our trial 
> onsets
> > > > > are not time-locked to our TR. We are also unsure how long our
> > > > > response window should be given our rather long trial duration
> > (12s).
> > > > > The code below is what I have made to try to do this and I keep
> > > > > getting that the schedules were ill-conditioned. Any 
> information on
> > > > > how to resolve this error is appreciated!
> > > > >
> > > > > /./optseq2 --ntp 180 --tr 2 --psdwin 0 30 1 --ev  flexibility 
> 12 10
> > > > > --ev control 12 10 --nsearch 10000 --nkeep 3 --o
> > > cFIST_10trials8s_Run1/
> > > > >
> > > > > //
> > > > >
> > > > > Thank you,
> > > > >
> > > > > *Bryce Dirks*
> > > > > Research Associate
> > > > > Brain Connectivity and Cognition Laboratory
> > > > > Department of Psychology
> > > > > University of Miami
> > > > > Website:
> > > >
> > >
> > 
> https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.psy.miami.edu%2Fbccl%2F&data=02%7C01%7Cbrd47%40miami.edu%7C4536742e42f64289da3308d547375f81%7C2a144b72f23942d48c0e6f0f17c48e33%7C0%7C0%7C636493225510541884&sdata=nNf5Fj9zXwtyGwSAu9Fv5XFUNJmDpwaYe8t0DeyIwF4%3D&reserved=0
> > > > > Phone:_ (305)284-3286_
> > > > >
> > > > >
> > > > >
> > > > >
> > > > > _______________________________________________
> > > > > Freesurfer mailing list
> > > > > Freesurfer@nmr.mgh.harvard.edu
> > > > >
> > > >
> > >
> > 
> https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer&data=02%7C01%7Cbrd47%40miami.edu%7C4536742e42f64289da3308d547375f81%7C2a144b72f23942d48c0e6f0f17c48e33%7C0%7C0%7C636493225510541884&sdata=fSxKgs2875NMsNRDDpEm4A3edizRkTK16%2BdRtSRGi9g%3D&reserved=0
> > > >
> > > > --
> > > > Douglas N. Greve, Ph.D.
> > > > MGH-NMR Center
> > > > gr...@nmr.mgh.harvard.edu
> > > > Phone Number: 617-724-2358
> > > > Fax: 617-726-7422
> > > >
> > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> > > > FileDrop:
> > > >
> > >
> > 
> https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgate.nmr.mgh.harvard.edu%2Ffiledrop2&data=02%7C01%7Cbrd47%40miami.edu%7C4536742e42f64289da3308d547375f81%7C2a144b72f23942d48c0e6f0f17c48e33%7C0%7C0%7C636493225510541884&sdata=Po9xHg28xXgZ%2Fsl18qFb2c4SQUL5vJY59lEdS7Y0Jj0%3D&reserved=0
> > > >
> > >
> > 
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> > > > Outgoing:
> > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> > > >
> > > > _______________________________________________
> > > > Freesurfer mailing list
> > > > Freesurfer@nmr.mgh.harvard.edu
> > > >
> > >
> > 
> https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer&data=02%7C01%7Cbrd47%40miami.edu%7C4536742e42f64289da3308d547375f81%7C2a144b72f23942d48c0e6f0f17c48e33%7C0%7C0%7C636493225510541884&sdata=fSxKgs2875NMsNRDDpEm4A3edizRkTK16%2BdRtSRGi9g%3D&reserved=0
> > > >
> > > >
> > > > The information in this e-mail is intended only for the person 
> to whom
> > > > it is
> > > > addressed. If you believe this e-mail was sent to you in error 
> and the
> > > > e-mail
> > > > contains patient information, please contact the Partners Compliance
> > > > HelpLine at
> > > >
> > >
> > 
> https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.partners.org%2Fcomplianceline&data=02%7C01%7Cbrd47%40miami.edu%7C4536742e42f64289da3308d547375f81%7C2a144b72f23942d48c0e6f0f17c48e33%7C0%7C0%7C636493225510541884&sdata=V8NCrEqLIkEyHtlLSmUaoJmjbF55EbLjNeXeXzeDMRs%3D&reserved=0
>  
>
> >
> > >
> > > > . If the e-mail was sent to you in error
> > > > but does not contain patient information, please contact the sender
> > > > and properly
> > > > dispose of the e-mail.
> > > >
> > > >
> > > >
> > > > _______________________________________________
> > > > Freesurfer mailing list
> > > > Freesurfer@nmr.mgh.harvard.edu
> > > >
> > >
> > 
> https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer&data=02%7C01%7Cbrd47%40miami.edu%7Ce895fb97ad7d43cec71808d547ea050d%7C2a144b72f23942d48c0e6f0f17c48e33%7C0%7C0%7C636493992801342342&sdata=mHHQHUrpvioGIXd2MzfgLK4w0l25eMUXuKpnpbqSVYk%3D&reserved=0
> > >
> > > --
> > > Douglas N. Greve, Ph.D.
> > > MGH-NMR Center
> > > gr...@nmr.mgh.harvard.edu
> > > Phone Number: 617-724-2358
> > > Fax: 617-726-7422
> > >
> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> > > FileDrop:
> > >
> > 
> https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgate.nmr.mgh.harvard.edu%2Ffiledrop2&data=02%7C01%7Cbrd47%40miami.edu%7Ce895fb97ad7d43cec71808d547ea050d%7C2a144b72f23942d48c0e6f0f17c48e33%7C0%7C0%7C636493992801342342&sdata=Ftat5sm0dLoERtVWNExcSACeoMlUlHhpmzbgRGYsfyk%3D&reserved=0
> > >
> > 
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> > > Outgoing: 
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> > >
> > > _______________________________________________
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> > >
> > 
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> > >
> > >
> > > The information in this e-mail is intended only for the person to whom
> > > it is
> > > addressed. If you believe this e-mail was sent to you in error and the
> > > e-mail
> > > contains patient information, please contact the Partners Compliance
> > > HelpLine at
> > >
> > 
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>  
>
> >
> > > . If the e-mail was sent to you in error
> > > but does not contain patient information, please contact the sender
> > > and properly
> > > dispose of the e-mail.
> > >
> > >
> > >
> > > _______________________________________________
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> > >
> > 
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> >
> > --
> > Douglas N. Greve, Ph.D.
> > MGH-NMR Center
> > gr...@nmr.mgh.harvard.edu
> > Phone Number: 617-724-2358
> > Fax: 617-726-7422
> >
> > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> > FileDrop:
> > 
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> > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> >
> > _______________________________________________
> > Freesurfer mailing list
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> > 
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> >
> >
> > The information in this e-mail is intended only for the person to whom
> > it is
> > addressed. If you believe this e-mail was sent to you in error and the
> > e-mail
> > contains patient information, please contact the Partners Compliance
> > HelpLine at
> > 
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>  
>
> > . If the e-mail was sent to you in error
> > but does not contain patient information, please contact the sender
> > and properly
> > dispose of the e-mail.
> >
> >
> >
> > _______________________________________________
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > 
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>
> -- 
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: 
> https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgate.nmr.mgh.harvard.edu%2Ffiledrop2&data=02%7C01%7Cbrd47%40miami.edu%7Cbc30d90ba26d41b342f508d54802dacc%7C2a144b72f23942d48c0e6f0f17c48e33%7C0%7C0%7C636494099467047925&sdata=Bn3jrQ4NlKosWJcK0EIrHkZA5ZFUvDVQRBwFaInjLZQ%3D&reserved=0
> https://na01.safelinks.protection.outlook.com/?url=www.nmr.mgh.harvard.edu%2Ffacility%2Ffiledrop%2Findex.html&data=02%7C01%7Cbrd47%40miami.edu%7Cbc30d90ba26d41b342f508d54802dacc%7C2a144b72f23942d48c0e6f0f17c48e33%7C0%7C0%7C636494099467047925&sdata=wpc0O%2BbCQZcgC%2B%2FOjQuk1jg%2BnPPoIk2fny3C%2FjkUDRQ%3D&reserved=0
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
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>
>
> The information in this e-mail is intended only for the person to whom 
> it is
> addressed. If you believe this e-mail was sent to you in error and the 
> e-mail
> contains patient information, please contact the Partners Compliance 
> HelpLine at
> https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.partners.org%2Fcomplianceline&data=02%7C01%7Cbrd47%40miami.edu%7Cbc30d90ba26d41b342f508d54802dacc%7C2a144b72f23942d48c0e6f0f17c48e33%7C0%7C0%7C636494099467047925&sdata=xpNvtKkppT%2FpWDzBfsNZtnLuksvn0mBwQWJgjVaeR5I%3D&reserved=0
>  
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-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

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